AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1161470


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1161470 MtrunA17_Chr7g0255191 70.238 84 20 2 11 94 1 79 3.44e-28 106
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 18 sgRNAs with CRISPR-Local

Find 134 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTATTTCGATTGTGAGGC+AGG 0.378148 7_4:+51680930 None:intergenic
ATTTCTTGAATTTGATCTAC+AGG 0.440894 7_4:-51680896 Msa1161470:CDS
TGCTGGAGCTGGAGGATTGT+GGG 0.444109 7_4:-51680863 Msa1161470:CDS
GAATGTTGTGAAGAGAGAAA+TGG 0.456469 7_4:-51681441 Msa1161470:CDS
GAGATCAATCATGCTGGAGC+TGG 0.463454 7_4:-51680874 Msa1161470:CDS
GTTAATTGTGGTTTGTCTTG+TGG 0.472056 7_4:-51681378 Msa1161470:CDS
AATGTTGTGAAGAGAGAAAT+GGG 0.485564 7_4:-51681440 Msa1161470:CDS
GAGAGAAATGGGTTGTTCAA+AGG 0.494479 7_4:-51681429 Msa1161470:CDS
GTGCATGTTTGTATTTGAGT+TGG 0.504300 7_4:-51680953 Msa1161470:CDS
ATGCTTTGATGTGCAAGTGC+AGG 0.534577 7_4:-51681351 Msa1161470:CDS
ACCTCTGTTGCTCACAAGCT+CGG 0.539869 7_4:+51680840 None:intergenic
ATCAATCATGCTGGAGCTGG+AGG 0.547119 7_4:-51680871 Msa1161470:CDS
ATGCTGGAGCTGGAGGATTG+TGG 0.558911 7_4:-51680864 Msa1161470:CDS
TATGCTGCAACTGTTAATTG+TGG 0.563050 7_4:-51681390 Msa1161470:CDS
CTACAGGAGATCAATCATGC+TGG 0.591320 7_4:-51680880 Msa1161470:CDS
GCCGAGCTTGTGAGCAACAG+AGG 0.602025 7_4:-51680841 Msa1161470:CDS
TTTCTGCTATTTCGATTGTG+AGG 0.603002 7_4:+51680926 None:intergenic
GGCTGATTTAAATGCAACAC+TGG 0.605166 7_4:-51681330 Msa1161470:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTCTTTAATATAATAACT+TGG + chr7_4:51681708-51681727 None:intergenic 10.0%
!! AAGTTATTATATTAAAGAAA+AGG - chr7_4:51681707-51681726 Msa1161470:intron 10.0%
!!! AGAAAATTAGATTTTATTAT+AGG - chr7_4:51681802-51681821 Msa1161470:intron 10.0%
!!! TTTTCTTTAATATAATAACT+TGG + chr7_4:51681708-51681727 None:intergenic 10.0%
!! AAGTTATTATATTAAAGAAA+AGG - chr7_4:51681707-51681726 Msa1161470:intron 10.0%
!!! AGAAAATTAGATTTTATTAT+AGG - chr7_4:51681802-51681821 Msa1161470:intron 10.0%
!! AGTATGTATATATTATTATG+AGG + chr7_4:51681028-51681047 None:intergenic 15.0%
!! AAAATAATTATCAAGTCAAA+GGG + chr7_4:51681058-51681077 None:intergenic 15.0%
!! AAAAATAATTATCAAGTCAA+AGG + chr7_4:51681059-51681078 None:intergenic 15.0%
!!! TATGATTCATTTTTCTTATA+TGG - chr7_4:51681078-51681097 Msa1161470:intron 15.0%
!! AGTATGTATATATTATTATG+AGG + chr7_4:51681028-51681047 None:intergenic 15.0%
!! AAAATAATTATCAAGTCAAA+GGG + chr7_4:51681058-51681077 None:intergenic 15.0%
!! AAAAATAATTATCAAGTCAA+AGG + chr7_4:51681059-51681078 None:intergenic 15.0%
!!! TATGATTCATTTTTCTTATA+TGG - chr7_4:51681078-51681097 Msa1161470:intron 15.0%
!! AATAGAACATAGCAAAAAAA+AGG - chr7_4:51681156-51681175 Msa1161470:intron 20.0%
!! CATATTGTAACATTATTAAG+CGG - chr7_4:51681195-51681214 Msa1161470:intron 20.0%
!! AGAATACTAAACAAGTTAAA+AGG + chr7_4:51681272-51681291 None:intergenic 20.0%
!! TCCTAAGTAGATTAAAATAA+AGG - chr7_4:51681611-51681630 Msa1161470:intron 20.0%
!!! TCCTTTATTTTAATCTACTT+AGG + chr7_4:51681615-51681634 None:intergenic 20.0%
!! AATAGAACATAGCAAAAAAA+AGG - chr7_4:51681156-51681175 Msa1161470:intron 20.0%
!! CATATTGTAACATTATTAAG+CGG - chr7_4:51681195-51681214 Msa1161470:intron 20.0%
!! AGAATACTAAACAAGTTAAA+AGG + chr7_4:51681272-51681291 None:intergenic 20.0%
!! TCCTAAGTAGATTAAAATAA+AGG - chr7_4:51681611-51681630 Msa1161470:intron 20.0%
!!! TCCTTTATTTTAATCTACTT+AGG + chr7_4:51681615-51681634 None:intergenic 20.0%
!!! GTTTAAGATTTTCTTGCTTT+GGG + chr7_4:51680832-51680851 None:intergenic 25.0%
! GTTGAATTTATAGAGAAACA+AGG + chr7_4:51680974-51680993 None:intergenic 25.0%
!!! TCTTTTTGGAATATTCTTTG+AGG - chr7_4:51681515-51681534 Msa1161470:intron 25.0%
!!! ACAGATATTGTTGATGATAT+GGG - chr7_4:51681568-51681587 Msa1161470:intron 25.0%
! ATTTCTTGAATTTGATCTAC+AGG - chr7_4:51681883-51681902 Msa1161470:intron 25.0%
!!! GTTTAAGATTTTCTTGCTTT+GGG + chr7_4:51680832-51680851 None:intergenic 25.0%
! GTTGAATTTATAGAGAAACA+AGG + chr7_4:51680974-51680993 None:intergenic 25.0%
!!! TCTTTTTGGAATATTCTTTG+AGG - chr7_4:51681515-51681534 Msa1161470:intron 25.0%
!!! ACAGATATTGTTGATGATAT+GGG - chr7_4:51681568-51681587 Msa1161470:intron 25.0%
! ATTTCTTGAATTTGATCTAC+AGG - chr7_4:51681883-51681902 Msa1161470:intron 25.0%
!! GGTTTAAGATTTTCTTGCTT+TGG + chr7_4:51680833-51680852 None:intergenic 30.0%
AAGTGAGTTATGAATGTGTT+TGG + chr7_4:51680854-51680873 None:intergenic 30.0%
TTGGTCTGAATAATGAATGA+AGG + chr7_4:51680945-51680964 None:intergenic 30.0%
TAGAGAAACAAGGATTGAAT+TGG + chr7_4:51680964-51680983 None:intergenic 30.0%
TCAGTCACAAGATATGTAAA+AGG + chr7_4:51681123-51681142 None:intergenic 30.0%
! ACATAGCAAAAAAAAGGTGT+CGG - chr7_4:51681162-51681181 Msa1161470:intron 30.0%
ATTGTAACATTATTAAGCGG+TGG - chr7_4:51681198-51681217 Msa1161470:intron 30.0%
!! CTAGTGTTAGTTAACTTGTT+TGG - chr7_4:51681235-51681254 Msa1161470:intron 30.0%
AATGTTGTGAAGAGAGAAAT+GGG - chr7_4:51681339-51681358 Msa1161470:CDS 30.0%
AATATTCCAAAAAGAGTCTC+CGG + chr7_4:51681510-51681529 None:intergenic 30.0%
!! CACAGATATTGTTGATGATA+TGG - chr7_4:51681567-51681586 Msa1161470:intron 30.0%
AGTACATAAGACTATAAGAC+TGG - chr7_4:51681639-51681658 Msa1161470:intron 30.0%
ATTATCGTCTATTGCATTTG+TGG - chr7_4:51681739-51681758 Msa1161470:intron 30.0%
TGAATGAACTACATAGAACT+TGG - chr7_4:51681773-51681792 Msa1161470:intron 30.0%
!! GGTTTAAGATTTTCTTGCTT+TGG + chr7_4:51680833-51680852 None:intergenic 30.0%
AAGTGAGTTATGAATGTGTT+TGG + chr7_4:51680854-51680873 None:intergenic 30.0%
TTGGTCTGAATAATGAATGA+AGG + chr7_4:51680945-51680964 None:intergenic 30.0%
TAGAGAAACAAGGATTGAAT+TGG + chr7_4:51680964-51680983 None:intergenic 30.0%
TCAGTCACAAGATATGTAAA+AGG + chr7_4:51681123-51681142 None:intergenic 30.0%
! ACATAGCAAAAAAAAGGTGT+CGG - chr7_4:51681162-51681181 Msa1161470:intron 30.0%
ATTGTAACATTATTAAGCGG+TGG - chr7_4:51681198-51681217 Msa1161470:intron 30.0%
!! CTAGTGTTAGTTAACTTGTT+TGG - chr7_4:51681235-51681254 Msa1161470:intron 30.0%
AATGTTGTGAAGAGAGAAAT+GGG - chr7_4:51681339-51681358 Msa1161470:CDS 30.0%
AATATTCCAAAAAGAGTCTC+CGG + chr7_4:51681510-51681529 None:intergenic 30.0%
!! CACAGATATTGTTGATGATA+TGG - chr7_4:51681567-51681586 Msa1161470:intron 30.0%
AGTACATAAGACTATAAGAC+TGG - chr7_4:51681639-51681658 Msa1161470:intron 30.0%
ATTATCGTCTATTGCATTTG+TGG - chr7_4:51681739-51681758 Msa1161470:intron 30.0%
TGAATGAACTACATAGAACT+TGG - chr7_4:51681773-51681792 Msa1161470:intron 30.0%
AGTGAAGATAGAGTGATGTT+GGG + chr7_4:51680919-51680938 None:intergenic 35.0%
AAGTGAAGATAGAGTGATGT+TGG + chr7_4:51680920-51680939 None:intergenic 35.0%
GAATGTTGTGAAGAGAGAAA+TGG - chr7_4:51681338-51681357 Msa1161470:CDS 35.0%
TATGCTGCAACTGTTAATTG+TGG - chr7_4:51681389-51681408 Msa1161470:CDS 35.0%
! GTTAATTGTGGTTTGTCTTG+TGG - chr7_4:51681401-51681420 Msa1161470:CDS 35.0%
TTAATCTACTTAGGATGTCG+CGG + chr7_4:51681606-51681625 None:intergenic 35.0%
ACATAAGACTATAAGACTGG+AGG - chr7_4:51681642-51681661 Msa1161470:intron 35.0%
CATAAGACTATAAGACTGGA+GGG - chr7_4:51681643-51681662 Msa1161470:intron 35.0%
AACCATGTAATAACTGAGTC+AGG + chr7_4:51681677-51681696 None:intergenic 35.0%
GTGCATGTTTGTATTTGAGT+TGG - chr7_4:51681826-51681845 Msa1161470:intron 35.0%
!! TTTCTGCTATTTCGATTGTG+AGG + chr7_4:51681856-51681875 None:intergenic 35.0%
AGTGAAGATAGAGTGATGTT+GGG + chr7_4:51680919-51680938 None:intergenic 35.0%
AAGTGAAGATAGAGTGATGT+TGG + chr7_4:51680920-51680939 None:intergenic 35.0%
GAATGTTGTGAAGAGAGAAA+TGG - chr7_4:51681338-51681357 Msa1161470:CDS 35.0%
TATGCTGCAACTGTTAATTG+TGG - chr7_4:51681389-51681408 Msa1161470:CDS 35.0%
! GTTAATTGTGGTTTGTCTTG+TGG - chr7_4:51681401-51681420 Msa1161470:CDS 35.0%
TTAATCTACTTAGGATGTCG+CGG + chr7_4:51681606-51681625 None:intergenic 35.0%
ACATAAGACTATAAGACTGG+AGG - chr7_4:51681642-51681661 Msa1161470:intron 35.0%
CATAAGACTATAAGACTGGA+GGG - chr7_4:51681643-51681662 Msa1161470:intron 35.0%
AACCATGTAATAACTGAGTC+AGG + chr7_4:51681677-51681696 None:intergenic 35.0%
GTGCATGTTTGTATTTGAGT+TGG - chr7_4:51681826-51681845 Msa1161470:intron 35.0%
!! TTTCTGCTATTTCGATTGTG+AGG + chr7_4:51681856-51681875 None:intergenic 35.0%
!! TTGCTTTGGGTTGTGTTTGT+GGG + chr7_4:51680819-51680838 None:intergenic 40.0%
! TGGATTTGGGTTTGCTTCTA+CGG + chr7_4:51680894-51680913 None:intergenic 40.0%
GTGATGTTGGGTTTGGATTT+GGG + chr7_4:51680907-51680926 None:intergenic 40.0%
AGTGATGTTGGGTTTGGATT+TGG + chr7_4:51680908-51680927 None:intergenic 40.0%
AGATAGAGTGATGTTGGGTT+TGG + chr7_4:51680914-51680933 None:intergenic 40.0%
GAGTGAGTGAGTGATGAATT+TGG + chr7_4:51680996-51681015 None:intergenic 40.0%
!! GAGAGAAATGGGTTGTTCAA+AGG - chr7_4:51681350-51681369 Msa1161470:CDS 40.0%
! GGCTGATTTAAATGCAACAC+TGG - chr7_4:51681449-51681468 Msa1161470:CDS 40.0%
! TTGATGATATGGGCTGTAGA+AGG - chr7_4:51681578-51681597 Msa1161470:intron 40.0%
AGCCTGACTCAGTTATTACA+TGG - chr7_4:51681672-51681691 Msa1161470:intron 40.0%
!! TTGCTTTGGGTTGTGTTTGT+GGG + chr7_4:51680819-51680838 None:intergenic 40.0%
! TGGATTTGGGTTTGCTTCTA+CGG + chr7_4:51680894-51680913 None:intergenic 40.0%
GTGATGTTGGGTTTGGATTT+GGG + chr7_4:51680907-51680926 None:intergenic 40.0%
AGTGATGTTGGGTTTGGATT+TGG + chr7_4:51680908-51680927 None:intergenic 40.0%
AGATAGAGTGATGTTGGGTT+TGG + chr7_4:51680914-51680933 None:intergenic 40.0%
GAGTGAGTGAGTGATGAATT+TGG + chr7_4:51680996-51681015 None:intergenic 40.0%
!! GAGAGAAATGGGTTGTTCAA+AGG - chr7_4:51681350-51681369 Msa1161470:CDS 40.0%
! GGCTGATTTAAATGCAACAC+TGG - chr7_4:51681449-51681468 Msa1161470:CDS 40.0%
! TTGATGATATGGGCTGTAGA+AGG - chr7_4:51681578-51681597 Msa1161470:intron 40.0%
AGCCTGACTCAGTTATTACA+TGG - chr7_4:51681672-51681691 Msa1161470:intron 40.0%
!! CTTGCTTTGGGTTGTGTTTG+TGG + chr7_4:51680820-51680839 None:intergenic 45.0%
! TTTGGGTTTGCTTCTACGGT+TGG + chr7_4:51680890-51680909 None:intergenic 45.0%
ATGCTTTGATGTGCAAGTGC+AGG - chr7_4:51681428-51681447 Msa1161470:CDS 45.0%
ACTGGTTGTAGATGCTTCTC+AGG - chr7_4:51681467-51681486 Msa1161470:intron 45.0%
! CGAATACCGGAGACTCTTTT+TGG - chr7_4:51681501-51681520 Msa1161470:intron 45.0%
!! TGCTATTTCGATTGTGAGGC+AGG + chr7_4:51681852-51681871 None:intergenic 45.0%
CTACAGGAGATCAATCATGC+TGG - chr7_4:51681899-51681918 Msa1161470:intron 45.0%
!! CTTGCTTTGGGTTGTGTTTG+TGG + chr7_4:51680820-51680839 None:intergenic 45.0%
! TTTGGGTTTGCTTCTACGGT+TGG + chr7_4:51680890-51680909 None:intergenic 45.0%
ATGCTTTGATGTGCAAGTGC+AGG - chr7_4:51681428-51681447 Msa1161470:CDS 45.0%
ACTGGTTGTAGATGCTTCTC+AGG - chr7_4:51681467-51681486 Msa1161470:intron 45.0%
! CGAATACCGGAGACTCTTTT+TGG - chr7_4:51681501-51681520 Msa1161470:intron 45.0%
!! TGCTATTTCGATTGTGAGGC+AGG + chr7_4:51681852-51681871 None:intergenic 45.0%
CTACAGGAGATCAATCATGC+TGG - chr7_4:51681899-51681918 Msa1161470:intron 45.0%
GTAGATGCTTCTCAGGCATC+TGG - chr7_4:51681474-51681493 Msa1161470:intron 50.0%
GGCATCTGGAAGACGAATAC+CGG - chr7_4:51681488-51681507 Msa1161470:intron 50.0%
GAGATCAATCATGCTGGAGC+TGG - chr7_4:51681905-51681924 Msa1161470:intron 50.0%
ATCAATCATGCTGGAGCTGG+AGG - chr7_4:51681908-51681927 Msa1161470:intron 50.0%
ACCTCTGTTGCTCACAAGCT+CGG + chr7_4:51681942-51681961 None:intergenic 50.0%
GTAGATGCTTCTCAGGCATC+TGG - chr7_4:51681474-51681493 Msa1161470:intron 50.0%
GGCATCTGGAAGACGAATAC+CGG - chr7_4:51681488-51681507 Msa1161470:intron 50.0%
GAGATCAATCATGCTGGAGC+TGG - chr7_4:51681905-51681924 Msa1161470:intron 50.0%
ATCAATCATGCTGGAGCTGG+AGG - chr7_4:51681908-51681927 Msa1161470:intron 50.0%
ACCTCTGTTGCTCACAAGCT+CGG + chr7_4:51681942-51681961 None:intergenic 50.0%
ATGCTGGAGCTGGAGGATTG+TGG - chr7_4:51681915-51681934 Msa1161470:intron 55.0%
TGCTGGAGCTGGAGGATTGT+GGG - chr7_4:51681916-51681935 Msa1161470:intron 55.0%
ATGCTGGAGCTGGAGGATTG+TGG - chr7_4:51681915-51681934 Msa1161470:intron 55.0%
TGCTGGAGCTGGAGGATTGT+GGG - chr7_4:51681916-51681935 Msa1161470:intron 55.0%
GCCGAGCTTGTGAGCAACAG+AGG - chr7_4:51681938-51681957 Msa1161470:intron 60.0%
GCCGAGCTTGTGAGCAACAG+AGG - chr7_4:51681938-51681957 Msa1161470:intron 60.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 51680810 51681991 51680810 ID=Msa1161470;Name=Msa1161470
chr7_4 mRNA 51680810 51681991 51680810 ID=Msa1161470-mRNA-1;Parent=Msa1161470;Name=Msa1161470-mRNA-1;_AED=0.63;_eAED=0.63;_QI=0|0|0|0.66|1|1|3|0|103
chr7_4 exon 51681988 51681991 51681988 ID=Msa1161470-mRNA-1:exon:14695;Parent=Msa1161470-mRNA-1
chr7_4 exon 51681331 51681470 51681331 ID=Msa1161470-mRNA-1:exon:14694;Parent=Msa1161470-mRNA-1
chr7_4 exon 51680810 51680977 51680810 ID=Msa1161470-mRNA-1:exon:14693;Parent=Msa1161470-mRNA-1
chr7_4 CDS 51681988 51681991 51681988 ID=Msa1161470-mRNA-1:cds;Parent=Msa1161470-mRNA-1
chr7_4 CDS 51681331 51681470 51681331 ID=Msa1161470-mRNA-1:cds;Parent=Msa1161470-mRNA-1
chr7_4 CDS 51680810 51680977 51680810 ID=Msa1161470-mRNA-1:cds;Parent=Msa1161470-mRNA-1
Gene Sequence

>Msa1161470

ATGGATAGATTGAATGTTGTGAAGAGAGAAATGGGTTGTTCAAAGGATTCATGCTGTGTTTTTATGCTGCAACTGTTAATTGTGGTTTGTCTTGTGGTTCAATGCTTTGATGTGCAAGTGCAGGCTGATTTAAATGCAACACTGGTGTGCATGTTTGTATTTGAGTTGGCCTGCCTCACAATCGAAATAGCAGAAAATGACGAATTTCTTGAATTTGATCTACAGGAGATCAATCATGCTGGAGCTGGAGGATTGTGGGCCGAGCTTGTGAGCAACAGAGGTCACTTTCATATTCTCTTAAATTTTAAATGA

Protein sequence

>Msa1161470

MDRLNVVKREMGCSKDSCCVFMLQLLIVVCLVVQCFDVQVQADLNATLVCMFVFELACLTIEIAENDEFLEFDLQEINHAGAGGLWAELVSNRGHFHILLNFK*